|
| Status |
Public on Oct 16, 2024 |
| Title |
parthenote1 BiSulfite-seq |
| Sample type |
SRA |
| |
|
| Source name |
whole embryo
|
| Organism |
Sus scrofa |
| Characteristics |
tissue: whole embryo
treatment: parthenogenesis
|
| Treatment protocol |
In a fusion chamber with 250 µm diameter wire electrodes, selected oocytes were placed and fusion was achieved by two DC pulses (1 sec interval) of 1.2 kV/cm for 30 µs using an LF101 Electro Cell Fusion Generator.
|
| Growth protocol |
After electric stimulation of oocytes followed by 2 h of stabilization period, parthenogenetic embryos were placed into oviducts of each of the two surrogate gilts aged 12 months at onset of estrus to produce developed parthenogenetic embryos.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
From the whole collected embryos of CN and PA, genomic DNA was isolated and fragmented.
For optimization of bisulfite conversion of genomic DNA, Accel-NGS Methyl-Seq DNA Library Kit (Swift Biosciences, Inc. Ann Arbor, MI, USA) was used according to the manufacturer`s instructions.
|
| |
|
| Library strategy |
Bisulfite-Seq |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
The raw WGBS reads were trimmed and filtered, using the default parameters of Trim Galore (v0.12.1).
The resulting cleaned reads were mapped to the pig reference genome (Sscrofa11.1/susScr11) using the Bismark aligner (v0.22.3) with default parameters.
Deduplication was performed with deduplicate_bismark and methylation percentages for cytosines in CpGs were determined using bismark_methylation_extractor.
Assembly: susScr11
Supplementary files format and content: methylation ratios in bedGraph format
|
| |
|
| Submission date |
Apr 08, 2024 |
| Last update date |
Oct 16, 2024 |
| Contact name |
Jinsoo Ahn |
| E-mail(s) |
[email protected]
|
| Organization name |
Ohio State Univesity
|
| Street address |
2029 Fyffe Rd
|
| City |
Columbus |
| ZIP/Postal code |
43210 |
| Country |
USA |
| |
|
| Platform ID |
GPL22918 |
| Series (1) |
| GSE263495 |
Lineage-specific genomic imprinting in the ZNF791 locus [BiSulfite-seq] |
|
| Relations |
| BioSample |
SAMN40874734 |
| SRA |
SRX24189416 |
